Journal of Diagnostics Concepts & Practice ›› 2020, Vol. 19 ›› Issue (1): 55-62.doi: 10.16150/j.1671-2870.2020.01.012
• Original articles • Previous Articles Next Articles
LI Hui1a, FENG Jie2, HAN Lizhong1b()
Received:
2018-09-30
Online:
2020-02-25
Published:
2020-02-25
Contact:
HAN Lizhong
E-mail:13916291150@163.com
CLC Number:
LI Hui, FENG Jie, HAN Lizhong. Analysis of intestinal microbial composition in specific pathogen free mice using high-throughput sequencing[J]. Journal of Diagnostics Concepts & Practice, 2020, 19(1): 55-62.
样本号 | 序列 | Alpha 多样性 | |||||
---|---|---|---|---|---|---|---|
OTU | Ace指数 | Chao1指数 | Coverage指数 | Shannon指数 | Simpson指数 | ||
1 | 25549 | 293 | 347(325,384) | 344(319,393) | 0.997 808 | 3.89(3.87,3.91) | 0.043 4(0.042 3,0.044 4) |
2 | 25549 | 238 | 293(269,338) | 313(273,398) | 0.998 121 | 4.24(4.23,4.26) | 0.022 8(0.022 3,0.023 3) |
3 | 25549 | 250 | 302(279,341) | 323(286,398) | 0.997 926 | 3.97(3.95,3.99) | 0.038 2(0.037 3,0.039 1) |
4 | 25549 | 229 | 285(261,326) | 291(260,353) | 0.997 886 | 3.48(3.46,3.50) | 0.082 9(0.080 5,0.085 3) |
5 | 25549 | 167 | 202(184,237) | 202(182,251) | 0.998 708 | 3.59(3.57,3.61) | 0.051 4(0.050 3,0.052 5) |
6 | 25549 | 192 | 277(249,319) | 250(220,312) | 0.998 043 | 2.71(2.69,2.73) | 0.157 6(0.154 6,0.160 7) |
7 | 25549 | 222 | 274(252,313) | 281(252,340) | 0.997 847 | 3.35(3.33,3.37) | 0.071 3(0.069 8,0.072 8) |
8 | 25549 | 212 | 265(242,305) | 259(235,308) | 0.998 082 | 3.26(3.24,3.28) | 0.092 3(0.089 9,0.094 6) |
10 | 25549 | 345 | 403(381,440) | 426(389,494) | 0.997 260 | 4.06(4.04,4.08) | 0.038 9(0.037 9,0.039 8) |
54 | 25549 | 342 | 424(394,473) | 459(406,556) | 0.996 986 | 4.21(4.20,4.23) | 0.027 2(0.026 6,0.027 8) |
55 | 25549 | 213 | 265(242,306) | 276(243,344) | 0.998 121 | 2.84(2.81,2.86) | 0.172 2(0.168 1,0.176 3) |
样本号 | 序列 | Alpha 多样性 | |||||
---|---|---|---|---|---|---|---|
OTU | Ace指数 | Chao1指数 | Coverage指数 | Shannon指数 | Simpson指数 | ||
9 | 25549 | 236 | 337(305,382) | 293(265,347) | 0.997 730 | 3.36(3.34,3.38) | 0.071 0(0.069 6,0.072 5) |
18 | 25549 | 315 | 367(346,403) | 372(344,426) | 0.997 730 | 3.99(3.97,4.01) | 0.045 4(0.044 1,0.046 6) |
19 | 25549 | 377 | 439(416,475) | 439(412,488) | 0.996 986 | 3.91(3.89,3.93) | 0.052 7(0.051 3,0.054 2) |
20 | 25549 | 474 | 535(513,569) | 535(509,582) | 0.996 947 | 4.82(4.80,4.84) | 0.015 3(0.014 9,0.015 6) |
41 | 25549 | 178 | 246(221,286) | 245(206,336) | 0.998 552 | 3.63(3.61,3.65) | 0.051 2(0.049 9,0.052 5) |
42 | 25549 | 164 | 182(172,204) | 181(170,210) | 0.999 139 | 3.56(3.54,3.57) | 0.053 6(0.052 3,0.054 9) |
43 | 25549 | 70 | 97(82,128) | 78(72,101) | 0.999 530 | 2.63(2.61,2.64) | 0.107 7(0.106 1,0.109 3) |
44 | 25549 | 95 | 157(132,199) | 122(105,168) | 0.999 021 | 2.92(2.91,2.93) | 0.070 9(0.070 1,0.071 7) |
45 | 25549 | 88 | 132(112,166) | 122(99,196) | 0.999 256 | 2.78(2.76,2.79) | 0.116 9(0.114 2,0.119 5) |
46 | 25549 | 81 | 92(85,115) | 111(89,193) | 0.999 452 | 2.84(2.82,2.85) | 0.090 3(0.088 8,0.091 8) |
47 | 25549 | 161 | 195(178,229) | 199(177,251) | 0.998 708 | 3.40(3.39,3.42) | 0.058 1(0.057 0,0.059 2) |
样本号 | 序列 | Alpha 多样性 | |||||
---|---|---|---|---|---|---|---|
OTU | Ace指数 | Chao1指数 | Coverage指数 | Shannon指数 | Simpson指数 | ||
21 | 25549 | 465 | 522(501,554) | 524(498,571) | 0.997 025 | 4.43(4.41,4.45) | 0.037 9(0.036 8,0.039 1) |
22 | 25549 | 449 | 518(494,555) | 510(485,554) | 0.996 595 | 4.52(4.50,4.54) | 0.022 9(0.022 3,0.023 6) |
28 | 25549 | 293 | 370(341,416) | 371(335,435) | 0.997 221 | 3.24(3.22,3.26) | 0.103 5(0.101 1,0.105 8) |
33 | 25549 | 76 | 239(187,314) | 176(119,309) | 0.998 317 | 0.43(0.41,0.44) | 0.803 3(0.797 1,0.809 4) |
34 | 25549 | 28 | 193(129,297) | 79(43,202) | 0.999 295 | 0.34(0.33,0.35) | 0.823 6(0.817 7,0.829 5) |
35 | 25549 | 57 | 155(115,222) | 98(74,158) | 0.998 748 | 0.41(0.40,0.42) | 0.805 3(0.799 2,0.811 4) |
36 | 25549 | 26 | 64(44,108) | 46(31,99) | 0.999 491 | 0.61(0.60,0.62) | 0.643 0(0.637 1,0.648 9) |
49 | 25549 | 165 | 193(178,226) | 199(178,253) | 0.998 904 | 3.57(3.55,3.59) | 0.055 3(0.054 0,0.056 6) |
50 | 25549 | 186 | 229(208,271) | 234(207,296) | 0.998 552 | 3.69(3.67,3.70) | 0.044 1(0.043 3,0.045 0) |
51 | 25549 | 206 | 242(225,276) | 288(241,402) | 0.998 474 | 3.71(3.69,3.72) | 0.054 6(0.053 1,0.056 1) |
52 | 25549 | 183 | 245(219,293) | 238(210,294) | 0.997 965 | 1.69(1.67,1.72) | 0.466 0(0.458 7,0.473 3) |
58 | 25549 | 178 | 216(198,251) | 209(192,250) | 0.998 630 | 2.94(2.91,2.96) | 0.146 9(0.143 1,0.150 6) |
59 | 25549 | 258 | 287(274,314) | 290(273,329) | 0.998 474 | 3.79(3.77,3.81) | 0.047 0(0.045 9,0.048 0) |
60 | 25549 | 272 | 318(299,351) | 309(290,346) | 0.997 965 | 3.93(3.92,3.95) | 0.035 5(0.034 8,0.036 2) |
61 | 25549 | 235 | 296(271,339) | 324(280,409) | 0.997 652 | 3.49(3.47,3.51) | 0.060 5(0.059 1,0.061 9) |
样本号 | 序列 | Alpha 多样性 | |||||
---|---|---|---|---|---|---|---|
OTU | Ace指数 | Chao1指数 | Coverage指数 | Shannon指数 | Simpson指数 | ||
23 | 25549 | 248 | 326(296,373) | 317(286,374) | 0.997 221 | 2.40(2.37,2.42) | 0.244 1(0.239 4,0.248 7) |
24 | 25549 | 313 | 366(345,401) | 353(334,390) | 0.997 652 | 4.17(4.15,4.18) | 0.028 4(0.027 8,0.029 0) |
25 | 25549 | 408 | 516(480,570) | 523(477,601) | 0.996 086 | 4.08(4.06,4.11) | 0.042 8(0.041 6,0.044 0) |
26 | 25549 | 435 | 492(472,524) | 482(462,519) | 0.996 986 | 4.25(4.23,4.27) | 0.031 3(0.030 6,0.032 0) |
27 | 25549 | 446 | 516(492,553) | 512(485,559) | 0.996 516 | 3.85(3.83,3.88) | 0.066 3(0.064 3,0.068 2) |
30 | 25549 | 439 | 508(484,545) | 535(494,605) | 0.996 595 | 4.42(4.40,4.44) | 0.030 5(0.029 5,0.031 5) |
31 | 25549 | 532 | 600(577,635) | 600(572,646) | 0.996 399 | 4.60(4.58,4.62) | 0.026 9(0.026 1,0.027 6) |
32 | 25549 | 264 | 331(305,376) | 320(294,369) | 0.997 534 | 3.36(3.34,3.38) | 0.102 8(0.100 0,0.105 5) |
39 | 25549 | 28 | 62(39,138) | 88(45,244) | 0.999 374 | 0.76(0.74,0.77) | 0.605 3(0.599 0,0.611 6) |
40 | 25549 | 21 | 40(26,94) | 32(24,69) | 0.999 609 | 0.94(0.93,0.95) | 0.474 8(0.470 3,0.479 2) |
65 | 25549 | 339 | 389(369,422) | 404(373,462) | 0.997 534 | 4.19(4.17,4.21) | 0.035 0(0.033 9,0.036 0) |
品系 | 样本号 | 序列 | Alpha 多样性 | |||||
---|---|---|---|---|---|---|---|---|
OTU | Ace指数 | Chao1指数 | Coverage指数 | Shannon指数 | Simpson指数 | |||
Nu/Nu | 11 | 25549 | 178 | 302(263,358) | 281(229,387) | 0.997 730 | 2.89(2.87,2.91) | 0.141 3(0.137 6,0.144 9) |
37 | 25549 | 136 | 159(146,191) | 165(146,219) | 0.999 139 | 3.28(3.26,3.30) | 0.094 3(0.091 7,0.096 9) | |
38 | 25549 | 242 | 263(252,285) | 266(252,301) | 0.998 787 | 4.07(4.05,4.08) | 0.029 5(0.028 9,0.030 0) | |
db | 12 | 25549 | 361 | 400(384,427) | 389(375,417) | 0.997 926 | 4.08(4.06,4.10) | 0.045 3(0.043 9,0.046 6) |
13 | 25549 | 392 | 465(439,507) | 477(440,542) | 0.996 790 | 4.2(4.18,4.22) | 0.033 2(0.032 4,0.034 0) | |
14 | 25549 | 412 | 523(488,575) | 502(467,559) | 0.995 851 | 3.65(3.63,3.67) | 0.067 0(0.065 6,0.068 5) |
品系 | 样本号 | 序列 | Alpha 多样性 | |||||
---|---|---|---|---|---|---|---|---|
OTU | Ace指数 | Chao1指数 | Coverage指数 | Shannon指数 | Simpson指数 | |||
Ob | 14 | 25549 | 412 | 523(488,575) | 502(467,559) | 0.995 851 | 3.65(3.63,3.67) | 0.067 0(0.065 6,0.068 5) |
15 | 25549 | 393 | 465(439,506) | 472(438,531) | 0.996 751 | 4.27(4.25,4.29) | 0.031 6(0.030 8,0.032 5) | |
16 | 25549 | 417 | 479(457,515) | 480(452,528) | 0.996 947 | 4.17(4.15,4.19) | 0.035 0(0.034 3,0.035 8) | |
EIIA-Cre | 29 | 25549 | 319 | 378(354,418) | 385(353,448) | 0.997 730 | 4.10(4.08,4.12) | 0.044 6(0.043 3,0.046 0) |
suid-beige | 48 | 25549 | 140 | 228(195,280) | 218(169,347) | 0.998 787 | 3.57(3.55,3.59) | 0.047 0(0.046 1,0.047 9) |
CBA | 53 | 25549 | 187 | 200(192,217) | 200(191,224) | 0.999 217 | 4.02(4.01,4.03) | 0.028 8(0.028 2,0.029 4) |
Fek-cre | 56 | 25549 | 285 | 340(318,377) | 348(318,404) | 0.997 534 | 3.55(3.53,3.57) | 0.071 3(0.069 5,0.073 1) |
FAH-Rage | 57 | 25549 | 409 | 459(440,492) | 469(441,520) | 0.997 417 | 4.32(4.30,4.34) | 0.033 6(0.032 7,0.034 5) |
NAV | 62 | 25549 | 217 | 249(233,281) | 278(243,360) | 0.998 552 | 4.04(4.02,4.05) | 0.028 7(0.028 2,0.029 2) |
Ai32 | 63 | 25549 | 324 | 378(355,417) | 396(361,465) | 0.997 730 | 4.34(4.32,4.36) | 0.026 9(0.026 3,0.027 6) |
菌属 | 样本ID | 品系 | 丰度(%) |
---|---|---|---|
葡萄球菌属 | 39 | C57BL/6 | 2.300 0 |
40 | 2.600 0 | ||
65 | 0.023 0 | ||
41 | BALB/c | 0.066 5. | |
42 | 0.043 1 | ||
59 | ICR | 0.020 0 | |
60 | 0.011 0 | ||
56 | Fek-cre | 0.010 0 | |
64 | Ai32 | 0.015 7 | |
假单胞菌属 | 19 | BALB/c | 0.386 6 |
41 | 0.055 0 | ||
54 | C57 | 0.044 5 | |
支原体 | 23 | C57BL/6 | 0.058 7 |
25 | 0.027 4 | ||
26 | 0.058 7 | ||
30 | 0.058 7 | ||
3 | C57 | 0.524 5 | |
4 | 3.867 0 | ||
7 | 0.524 5 | ||
8 | 1.937 5 | ||
9 | BALB/c | 0.160 5 | |
20 | 0.516 7 | ||
28 | ICR | 0.015 7 | |
49 | 1.561 7 | ||
51 | 1.557 8 | ||
棒状杆菌属 | 60 | ICR | 0.011 7 |
61 | 0.027 4 |
Megablast方法 | 筛选病原菌(属) | OUT数量 |
---|---|---|
Staphylococcus epidermidis ATCC 12228 chromosome, complete genome | 葡萄球菌属 | 2070 |
Staphylococcus lentus F1142 s6_trimmed_contig_24, whole genome shotgun sequence | 32 | |
Pseudomonadaceae bacterium B4199, complete genome | 假单胞菌属 | 135 |
Pseudomonas koreensis strain D26, complete genome | 4 | |
Pseudomonas fluorescens F113, complete genome | 36 | |
Mycoplasma mobile 163K complete genome | 支原体 | 12 |
Corynebacterium callunae DSM 20147, complete genome | 棒状杆菌属 | 14 |
Corynebacterium casei LMG S-19264, complete genome | 7 |
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